散布矩阵-MPI [英] Scatter a Matrix - MPI
问题描述
我尝试将矩阵逐行散布到所有处理器，但这导致了分段错误.我不知道自己在做什么错.这是我的代码
I tried scattering a matrix by row to all the processors but it resulted in a segmentation fault.. I don't know what i am doing wrong.. Here is my code
if(rank == 0) {
A_row = 10;
A_col = 10;
/* calculate the strip size */
strip_size = A_row / size;
/* genarate Matrix A */
A = (double **)malloc(sizeof(double*) * 10);
int k = 0;
for(i = 0; i < 10; i++) {
A[i] = (double*)malloc(sizeof(double) * 10);
for(j = 0; j < 10; j++) {
A[i][j] = k;
k++;
printf("%lf ", A[i][j]);
}
printf("\n");
}
}
/* Broadcasting the row, column size of Matrix A as well as strip size and Matrix B*/
MPI_Bcast(&A_row, 1, MPI_INT, 0, MPI_COMM_WORLD);
MPI_Bcast(&A_col, 1, MPI_INT, 0, MPI_COMM_WORLD);
MPI_Bcast(&strip_size, 1, MPI_INT, 0, MPI_COMM_WORLD);
/* defining a datatype for sub-matrix */
MPI_Type_vector(strip_size, A_col, A_col, MPI_DOUBLE, &strip);
MPI_Type_commit(&strip);
strip_A = (double **)malloc(sizeof(double*)*strip_size);
for(i= 0; i< strip_size; i++) {
strip_A[i] = (double*)malloc(sizeof(double)*A_col);
}
MPI_Scatter(&A[0][0], 1, strip, &strip_A[0][0], 1, strip, 0, MPI_COMM_WORLD);
for(i = 0; i < strip_size; i++) {
if(i == 0) {
printf("rank = %d\n", rank);
}
for(j = 0; j < A_col; j++) {
printf("%lf ", strip_A[i][j]);
}
printf("\n");
}
谁能告诉我是怎么回事...
Can anyone tell me what is wrong...
这是我运行时的错误
mpirun -np 2 ./a.out
0.000000 1.000000 2.000000 3.000000 4.000000 5.000000 6.000000 7.000000 8.000000 9.000000
10.000000 11.000000 12.000000 13.000000 14.000000 15.000000 16.000000 17.000000 18.000000 19.000000
20.000000 21.000000 22.000000 23.000000 24.000000 25.000000 26.000000 27.000000 28.000000 29.000000
30.000000 31.000000 32.000000 33.000000 34.000000 35.000000 36.000000 37.000000 38.000000 39.000000
40.000000 41.000000 42.000000 43.000000 44.000000 45.000000 46.000000 47.000000 48.000000 49.000000
50.000000 51.000000 52.000000 53.000000 54.000000 55.000000 56.000000 57.000000 58.000000 59.000000
60.000000 61.000000 62.000000 63.000000 64.000000 65.000000 66.000000 67.000000 68.000000 69.000000
70.000000 71.000000 72.000000 73.000000 74.000000 75.000000 76.000000 77.000000 78.000000 79.000000
80.000000 81.000000 82.000000 83.000000 84.000000 85.000000 86.000000 87.000000 88.000000 89.000000
90.000000 91.000000 92.000000 93.000000 94.000000 95.000000 96.000000 97.000000 98.000000 99.000000
rank = 1
42.000000 43.000000 44.000000 45.000000 46.000000 47.000000 48.000000 49.000000 0.000000 0.000000
52.000000 53.000000 54.000000 55.000000 56.000000 57.000000 58.000000 59.000000 0.000000 0.000000
0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000
0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000
0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000
[seismicmstm:07338] *** Process received signal *** [seismicmstm:07338] Signal:
Segmentation fault (11)
[seismicmstm:07338] Signal code:
(128) [seismicmstm:07338] Failing at
address: (nil)
-------------------------------------------------------------------------- mpirun noticed that process rank 1 with PID 7338 on node seismicmstm.cluster exited on signal 11 (Segmentation fault).
--------------------------------------------------------------------------
推荐答案
这里发生了几件事情.好消息是，最困难的工作-创建mpi数据类型以及MPI_Scatter调用的基本结构-是正确的.
There's a couple things going on here. The good news is that the hardest stuff -- getting the mpi data type created, and the basic structure of the MPI_Scatter call -- are correct.
第一个问题是MPI_Scatter行使用&(A [0] [0])-但是除了排名为零以外，您没有将A设置为指向任何东西！因此，您两次取消对随机指针的引用，就出现了段错误.
The first issue is that the MPI_Scatter line uses &(A[0][0]) -- but in all but rank zero, you haven't set A to point to anything! So you dereference a random pointer twice, and there's your segfault.
suszterpatt建议的一个更微妙的问题是，不能保证分配的内存行是连续的，因此即使解决了上述问题，分散操作也可能无法正常工作.您正在尝试将strip_size * A_col双精度数从A中的某个位置发送到strip_A，但是strip_A可能不包括这么多的双精度数-可能是A_col双精度数，然后是一些填充，然后是A_col双精度数-甚至不同的行可能散布在整个内存中.修复的三种方式为简便性(IMHO):(a)通过创建整个数组，然后创建二维C数组以指向正确的位置，使数据在内存中是连续的； (b)一次只发送一行；或(c)创建一个MPI数据类型，该数据类型实际上反映了数据在内存中的映射方式(可能是随机的).
A more subtle issue, as suggested by suszterpatt, is that there's no guarantee that your rows of allocated memory are contiguous, so your scatter operation may not work even if you fix the above. You are trying to send strip_size * A_col doubles from somewhere in A to strip_A, but strip_A may not consist of that many doubles contiguously - it could be A_col doubles, and then some padding, then A_col doubles -- or indeed, the various rows could be scattered all over memory. The three ways of fixing that are, in order of ease (IMHO): (a) make the data contiguous in memory by creating the entire array and then creating the two-d C arrays to point to the right places; (b) to just send one row at a time; or (c) to create an MPI data type that actually reflects how your data is mapped (perhaps randomly) in memory.
使用(a)的方法似乎可行(无论如何，对于A_row均除以大小)，如下所示:
An approach using (a) that seems to work (for A_row evenly divided by size, anyway) looks like below:
#include <stdio.h>
#include <mpi.h>
#include <stdlib.h>
int main(int argc, char** argv) {
int rank, size;
int strip_size, A_row, A_col;
double **A, **strip_A, *Adata, *stripdata;
MPI_Datatype strip;
int i,j;
MPI_Init(&argc,&argv) ;
MPI_Comm_rank(MPI_COMM_WORLD,&rank) ;
MPI_Comm_size(MPI_COMM_WORLD,&size) ;
if(rank == 0) {
A_row = 10;
A_col = 10;
/* calculate the strip size */
strip_size = A_row / size;
/* genarate Matrix A */
Adata = (double *)malloc(sizeof(double)*A_row*A_col);
A = (double **)malloc(sizeof(double*) * A_row);
for(i = 0; i < A_row; i++) {
A[i] = &(Adata[i*A_col]);
}
int k = 0;
for(i = 0; i < A_row; i++) {
for(j = 0; j < A_col; j++) {
A[i][j] = k;
k++;
}
}
}
/* Broadcasting the row, column size of Matrix A as well as strip size and Matrix B*/
MPI_Bcast(&A_row, 1, MPI_INT, 0, MPI_COMM_WORLD);
MPI_Bcast(&A_col, 1, MPI_INT, 0, MPI_COMM_WORLD);
MPI_Bcast(&strip_size, 1, MPI_INT, 0, MPI_COMM_WORLD);
/* defining a datatype for sub-matrix */
MPI_Type_vector(strip_size, A_col, A_col, MPI_DOUBLE, &strip);
MPI_Type_commit(&strip);
stripdata = (double *)malloc(sizeof(double)*strip_size*A_col);
strip_A = (double **)malloc(sizeof(double*)*strip_size);
for(i= 0; i< strip_size; i++) {
strip_A[i] = &(stripdata[i*A_col]);
}
MPI_Scatter(Adata, 1, strip, &(strip_A[0][0]), 1, strip, 0, MPI_COMM_WORLD);
//MPI_Scatter(Adata, A_col*strip_size, MPI_DOUBLE, &(strip_A[0][0]), A_col*strip_size, MPI_DOUBLE, 0, MPI_COMM_WORLD);
for(i = 0; i < strip_size; i++) {
if(i == 0) {
printf("rank = %d\n", rank);
}
for(j = 0; j < A_col; j++) {
printf("%lf ", strip_A[i][j]);
}
printf("\n");
}
MPI_Type_free(&strip);
free(strip_A);
free(stripdata);
free(Adata);
free(A);
return 0;
}
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